Vietnamese national traveling to China

Chris, if you don't leave the transit zone in HK Airport, you don't need the transit permit in HK.

I would like to take the ferry from HKIA to Dongguan.
I know you do not have to go through HK immigration.... But, 2 questions/worries.

1 how do I get my luggage if I dont leave the "terminal area"?

2. How will the VN check-in counter allow my wife to fly if she only has a China visa? As far as they are concerned, her travel ends in HK and no HK entry permit.

China entry permits for VN nationals are easy. HK is a seperate one that takes 1 month+.

Advice? Appreciated!

Chris, if so, I’m afraid both of you need to apply for transit entry permit for your transit in HK. If you submit your application to the embassy of PRC in Vietnam and the embassy deals with the application itself, it usually takes 4 working days. But if it is transferred to HK immigration department, as you said, one month+ will be needed.
Or you should fly to mainland PRC directly without transiting in HK. In this case, there won’t be any problem.